c-Myc is a transcription factor that is constitutively and aberrantly expressed in over 70% of human cancers. Its direct inhibition has been shown to trigger rapid tumor regression in mice with only mild and fully reversible side effects, suggesting this to be a viable therapeutic strategy. Here we reassess the challenges of directly targeting c-Myc, evaluate lessons learned from current inhibitors, and explore how future strategies such as miniaturisation of Omomyc and targeting E-box binding could facilitate translation of c-Myc inhibitors into the clinic.

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Taking the Myc out of cancer: toward therapeutic strategies to directly inhibit c-Myc

Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible, and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the ‘best fit’ for a desired application is crucial. Correspondingly, there must be a variety of chemistries — spanning a range of rates and other features — to choose from. Over the past few years, considerable strides have been made towards not only expanding the number of bioorthogonal chemistries but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in the development of bioorthogonal reactions, focusing on how principles of physical organic chemistry have guided probe design. The continued expansion of this toolset will provide precisely tuned reagents for manipulating bonds in distinct environments. Tagging and manipulating biomolecules in living systems requires precisely tuned, biocompatible reactions. This Review focuses on recent advances in the development of bioorthogonal reactions, with an emphasis on how mechanistic insights have driven the field.

Developing bioorthogonal probes to span a spectrum of reactivities

Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.

Genome-wide mapping of G-quadruplex structures with CUT&Tag

The oncogene Myc is deregulated in the majority of human tumors and drives numerous hallmarks of cancer. Despite its indisputable role in cancer development and maintenance, Myc is still undrugged. Developing a clinical inhibitor for Myc has been particularly challenging owing to its intrinsically disordered nature and lack of a binding pocket, coupled with concerns regarding potentially deleterious side effects in normal proliferating tissues. However, major breakthroughs in the development of Myc inhibitors have arisen in the last couple of years. Notably, the direct Myc inhibitor that we developed has just entered clinical trials. Celebrating this milestone, with this Perspective, we pay homage to the different strategies developed so far against Myc and all of the researchers focused on developing treatments for a target long deemed undruggable.

The long journey to bring a Myc inhibitor to the clinic.

A small-sized benzothiazole–indolium fluorescent probe: the study of interaction specificity targeting c-MYC promoter G-quadruplex structures and live cell imaging

It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple 'off switches' for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.

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DNA G-quadruplex structures: more than simple roadblocks to transcription?

https://pubs.rsc.org/en/content/articlepdf/2020/cc/d0cc02954h

A short peptide that preferentially binds c-MYC G-quadruplex DNA

The unexplored potential of quinone methides in chemical biology.

/pdf/long-range-dna-interactions-inter-molecular-g-quadruplexes-2k0zcf0l.pdf

Denise Liano

Papers

DNA G-quadruplex structures: more than simple roadblocks to transcription?

A short peptide that preferentially binds c-MYC G-quadruplex DNA

The unexplored potential of quinone methides in chemical biology.

Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance